DmeINT0021525 @ dm6
Intron Retention
Gene
FBgn0001215 | Hrb98DE
Description
The gene Heterogeneous nuclear ribonucleoprotein at 98DE is referred to in FlyBase by the symbol DmelHrb98DE (CG9983, FBgn0001215). It is a protein_coding_gene from Dmel. It has 7 annotated transcripts and 7 polypeptides (4 unique). Gene sequence location is 3R:28599834..28605777. Its molecular function is described by 7 unique terms, many of which group under: heterocyclic compound binding; organic cyclic compound binding; binding; nucleic acid binding; RNA binding. It is involved in the biological process described with 9 unique terms, many of which group under: reproduction; visual system development; female germ-line stem cell population maintenance; stem cell population maintenance; developmental process involved in reproduction. 35 alleles are reported. The phenotypes of these alleles manifest in: fat body; epidermal cell; skeletal muscle of thorax; larva; intracellular membrane-bounded organelle. The phenotypic classes of alleles include: increased mortality during development; phenotype; visible; flightless. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of moderately high expression. Peak expression observed within 00-18 hour embryonic stages, at stages throughout the pupal period, in adult female stages.
Coordinates
chr3R:28599834-28601195:+
Coord C1 exon
chr3R:28599834-28599999
Coord A exon
chr3R:28600000-28600705
Coord C2 exon
chr3R:28600706-28601195
Length
706 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
TGATAAAATCAATAATTTAGGAC
3' ss Score
4.79
Exon sequences
Seq C1 exon
TCAGTTTTAGGGAAGGGGTGCTACAGTGAGCGTCTTTCGTTCCCAGTGTCGTTATTTCTATAGTATTGCTGAGATATATATCAGAGCAGTAAAGATATTTAAATATAAGTTCTTCGAAATGGGTGGTCACGACAACTGGAACAATGGTCAAAATGAGGAGCAAGAT
Seq A exon
GTAAGTAGCACACAAAACCGCGACTGCACAGGGAAAAAACTCAGTTCGGCCATAATCCCAATATATATATATTTTGGTGATCAACGCGCTTTTACCCATGCGGCAACTAAAGTTGATGTGCTAAAGCATTTCGTTGCGGTTTTGTTACTTAAGACTAAGACTAACAGTAGTTGTATCTTAATAGTGCTAGGGAGTACGATGCTGTCGGTATTGGTTTCTCTTTTAGCTTTTTAGTGCAAAAGGCGTGATCAAGAATACACATGTTACACACATTTTTTAAGGCATGGTGAAAAGAAACAGGGCAGATATTGTAAAAGTATTGTATTGACAAGGGTGTCTGTCAACTTATCGTTATCGTTCTAGGTAGTATCGAATAGGTGCTGGGTTTAATCGGGTTGTAGAAACGGTCACACTGTATTCAGTTTTTTCATTCGTCTCGTGTGTCAGGGGACTTTCTCCATTTGCAATAGCAAAAAAAATAGTTAGATTAGAAGTTGTTCAACTTTTGCATTAGTAAAATGGTGAACTCGAACCAGAACCAGAACGGCAACTCCAATGGCCATGATGATGTAAGTAGTGGATATTAAGGGTCTAGAAATTTCCTGTAAGCTGGTGTCTCGCCTTGCCGGTCGCCATTTTGAAAATTACGCATGTGTCTCAAGGGCGGAAAGTGAGGTTATGGCCATTGATAAAATCAATAATTTAG
Seq C2 exon
GACTTTCCTCAGGACTCCATCACCGAGCCGGAGCATATGCGCAAGCTGTTCATCGGTGGCTTGGACTACCGTACCACCGACGAGAACCTAAAGGCTCACTTCGAGAAATGGGGCAACATCGTGGACGTGGTGGTCATGAAGGATCCGCGCACAAAGCGTTCCCGCGGATTCGGATTCATCACCTATTCCCACTCGAGCATGATTGATGAGGCCCAAAAGTCGCGTCCCCACAAGATCGACGGTCGAGTGGTGGAGCCCAAGCGCGCCGTTCCCCGTCAGGACATTGATTCCCCGAATGCCGGAGCCACCGTAAAGAAACTCTTTGTTGGCGCCCTCAAGGACGACCATGATGAGCAGAGCATCCGCGACTACTTCCAGCACTTTGGCAACATCGTCGACATCAACATAGTCATTGACAAGGAGACTGGCAAGAAACGCGGATTCGCCTTCGTCGAGTTCGACGACTACGATCCCGTGGACAAAGTTGTGT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0001215:FBtr0085298:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.263
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0007617=RRM_1=WD(100=42.7),PF0007617=RRM_1=PU(81.4=34.8)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0084667

Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0084668
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCGAAATGGGTGGTCACGAC
R:
CGGGGAATCAATGTCCTGACG
Band lengths:
348-1054
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Neural diversity
- Neurogenesis
- Neuronal activity
- Splicing factor regulation (brain)
- Splicing factor regulation (SL2)